Re: [gmx-users] problem with new sugar residue

Hi Carmen, Well, adding a residue to aminoacids.dat only makes sense for amino acids (although I admit to fiddle it sometimes, in which case it is usually best to make a local copy). But one thing with amino acids is that backbone -N(H)-Ca-C(O)- thing, which is referred to in the termini database.

Re: [gmx-users] problem with new sugar residue

Many thanks in advance,but the problem seems to be solved just by not including the new residue name in the aminoacids.dat file, despite the instruction to do so in sec.5.5.1 chapter 5 Topologies of the manual. Can you tell me if this procedure is correct? Thanks again Carmen > Hi Carmen, > > You r

Re: [gmx-users] problem with new sugar residue

Well, what's in the .rtp entry, and what's in your coordinate file? You probably have some inconsistency in your naming that's causing pdb2gmx to take issue. -Justin [EMAIL PROTECTED] wrote: I added a new sugar residue in ffG53a6.rtp file, and I included in the aminaocid.dat file. I got the

Re: [gmx-users] problem with new sugar residue

Hi Carmen, You really have to be careful to match the .rtp to the .pdb building block. pdb2gmx indicates that there's an atom in the .pdb file, which is not found in the [ CHIT ] entry in the .rtp file. If you want better help, you'll have to ask a better question: you should provide more details

[gmx-users] problem with new sugar residue

I added a new sugar residue in ffG53a6.rtp file, and I included in the aminaocid.dat file. I got the following problem using pdb2gmx : ... Program pdb2gmx, VERSION 3.3.2 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom O in r